Duncan finished just two points off the world championships in third place after the final round in France over the weekend.
Duncan (21) finished on 231 points overall, behind championship winner Kiara Fontanesi, of Italy, on 229, with Frenchwoman Livia Lancelot on 232 points.
Duncan, who went into the weekend carrying a knee injury, finished sixth in the opening race in controversial circumstances.
She was leading but took evasive action on the final lap when she came across five riders who had crashed on a hill.
Trying to avoid them, she crashed into a fence and eventually finished sixth.
The race jury initially ruled the results would be awarded on the placings from the lap before the track was blocked, when Duncan was in front.
But this was then changed and the results at the end of the race were reinstated.
Duncan was then sitting nine points off the lead, going into the final race.
She blitzed it, lapping all but one rider, including new world champion Fontanesi, to win by more than 46sec.
Her coach, Josh Coppins said it was disappointing way for Duncan’s season to end.
"Walking the track on Friday we knew that some girls would not get round if it got wet and that’s what happened. Saturday was unlucky but we all know these things can happen in racing. It was unfair and it was a real shame that it impacted the championship," Coppins said.
Coppins was saddened that it had now been two years in a row that controversial unfortunate incidents out of Duncan’s hands — call them bad luck, call them racing incidents, call them what you like — had cost her two world titles.
Last season, Duncan’s championship was derailed when an errantly positioned photographer blocked her path on a jump, causing her to crash and injure herself.
"It was pretty disappointing that mistakes from within the promoter and Federation of International Motorcycling FIM, Youthstream officials and the hosting French Federation of Motorcycling have impacted the championship yet again.
"I don’t want to sound like sour grapes. We gave it our all, we did everything we can. I just feel sorry for Courtney.
"I’m really proud of the way she handled it and to come out and dominate the second moto, and win by over 40 seconds, lap up to second place and lap the new world champion. It shows only what could have been."
Duncan has returned to her training base in Belgium and will give her body a rest.
She has torn the menicscus in one knee but it is unclear whether she will have her knee operated on in Europe or when she returns to New Zealand.
